What is the optimal frame size for the second and third generation protein secondary structure prediction methods? Justify your answer.

I remember it has something to do with the average length of alpha-helix. More specifically, 3 on both side of a site. So in total the frame length should be 7. But I can't remember the reason behind the argument.

What do you think?

According to what my professor said in class, 2nd and 3rd generation of protein secondary structure reconstruction relies on statistics data of several consecutive residues. I guess what he meant by "frame size", is how many adjacent residues we should take into account in the algorithm.

3 Answers
3

I know that if you want to predict a secondary structure of a transmembrane protein, then your window size should be 20 amino acids (this is the average length of 1 transmembrane alpha helix spanning through the membrane).

That's the problem of computational biology - sometimes it's difficult to find what exactly what a term means. But I think my professor asked for general protein secondary structure predication, not transmemebrane protein.
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ablmfDec 14 '11 at 22:12

OK, so 2 responses, each concerning different protein segments of different types/functions/structures, but not an answer really getting to the heart of the question. Because of the homework tag, I am tempted not to reply - this is something the student should accomplish on his/her own. So, I'll give a general answer to start you thinking. Basically, such a value - be it 7 or 20 for TMs or 13 - is determined empirically.